Starting phenix.real_space_refine on Tue Mar 19 05:00:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz8_20953/03_2024/6uz8_20953.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz8_20953/03_2024/6uz8_20953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz8_20953/03_2024/6uz8_20953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz8_20953/03_2024/6uz8_20953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz8_20953/03_2024/6uz8_20953.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz8_20953/03_2024/6uz8_20953.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 140 5.16 5 Cl 4 4.86 5 C 15280 2.51 5 N 3828 2.21 5 O 4064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A ASP 317": "OD1" <-> "OD2" Residue "A ASP 334": "OD1" <-> "OD2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ASP 590": "OD1" <-> "OD2" Residue "A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 609": "NH1" <-> "NH2" Residue "A ARG 629": "NH1" <-> "NH2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A ASP 739": "OD1" <-> "OD2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A ASP 908": "OD1" <-> "OD2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 299": "OE1" <-> "OE2" Residue "D ASP 317": "OD1" <-> "OD2" Residue "D ASP 334": "OD1" <-> "OD2" Residue "D ARG 360": "NH1" <-> "NH2" Residue "D ARG 437": "NH1" <-> "NH2" Residue "D ARG 485": "NH1" <-> "NH2" Residue "D PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D ARG 544": "NH1" <-> "NH2" Residue "D ASP 590": "OD1" <-> "OD2" Residue "D PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 609": "NH1" <-> "NH2" Residue "D ARG 629": "NH1" <-> "NH2" Residue "D PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 737": "OD1" <-> "OD2" Residue "D ASP 739": "OD1" <-> "OD2" Residue "D ARG 758": "NH1" <-> "NH2" Residue "D GLU 881": "OE1" <-> "OE2" Residue "D ASP 908": "OD1" <-> "OD2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ASP 210": "OD1" <-> "OD2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B ASP 317": "OD1" <-> "OD2" Residue "B ASP 334": "OD1" <-> "OD2" Residue "B ARG 360": "NH1" <-> "NH2" Residue "B ARG 437": "NH1" <-> "NH2" Residue "B ARG 485": "NH1" <-> "NH2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B ASP 590": "OD1" <-> "OD2" Residue "B PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B ASP 739": "OD1" <-> "OD2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "B GLU 881": "OE1" <-> "OE2" Residue "B ASP 908": "OD1" <-> "OD2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C ASP 317": "OD1" <-> "OD2" Residue "C ASP 334": "OD1" <-> "OD2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ARG 437": "NH1" <-> "NH2" Residue "C ARG 485": "NH1" <-> "NH2" Residue "C PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C ARG 544": "NH1" <-> "NH2" Residue "C ASP 590": "OD1" <-> "OD2" Residue "C PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 609": "NH1" <-> "NH2" Residue "C ARG 629": "NH1" <-> "NH2" Residue "C PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C ASP 739": "OD1" <-> "OD2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "C GLU 881": "OE1" <-> "OE2" Residue "C ASP 908": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23320 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 21, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 21, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 5801 Chain: "D" Number of atoms: 5693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 21, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 21, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 5801 Chain: "B" Number of atoms: 5693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 21, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 21, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 5801 Chain: "C" Number of atoms: 5693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 21, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 21, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 5801 Chain: "A" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'R0D': 1, 'SBM': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'R0D': 1, 'SBM': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'R0D': 1, 'SBM': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'R0D': 1, 'SBM': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 22.09, per 1000 atoms: 0.95 Number of scatterers: 23320 At special positions: 0 Unit cell: (128.544, 128.544, 173.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 140 16.00 P 4 15.00 O 4064 8.00 N 3828 7.00 C 15280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 258 " distance=2.04 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 258 " distance=2.04 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 258 " distance=2.04 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 258 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.32 Conformation dependent library (CDL) restraints added in 8.0 seconds 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5616 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 0 sheets defined 71.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.970A pdb=" N PHE A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 160 through 172 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 257 through 265 removed outlier: 3.668A pdb=" N LYS A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 281 Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.776A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 311 removed outlier: 3.639A pdb=" N ASN A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 335 removed outlier: 4.085A pdb=" N TYR A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 329 " --> pdb=" O CYS A 325 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.649A pdb=" N VAL A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 3.507A pdb=" N LEU A 368 " --> pdb=" O SER A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.604A pdb=" N VAL A 378 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 4.004A pdb=" N GLN A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.876A pdb=" N LEU A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 438 through 460 Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.768A pdb=" N ARG A 464 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 465 " --> pdb=" O ALA A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 461 through 465' Processing helix chain 'A' and resid 483 through 488 removed outlier: 4.090A pdb=" N LYS A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 483 through 488' Processing helix chain 'A' and resid 492 through 521 removed outlier: 3.767A pdb=" N GLU A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TRP A 514 " --> pdb=" O CYS A 510 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Proline residue: A 518 - end of helix removed outlier: 3.506A pdb=" N TYR A 521 " --> pdb=" O GLY A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 558 removed outlier: 3.842A pdb=" N LEU A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 606 removed outlier: 3.750A pdb=" N SER A 595 " --> pdb=" O PRO A 591 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.675A pdb=" N ILE A 610 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 611 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 614 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Proline residue: A 615 - end of helix Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.652A pdb=" N GLN A 624 " --> pdb=" O PHE A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 636 through 657 removed outlier: 3.980A pdb=" N ILE A 640 " --> pdb=" O LYS A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.924A pdb=" N TRP A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 removed outlier: 3.735A pdb=" N VAL A 691 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 692 " --> pdb=" O LYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 732 removed outlier: 3.580A pdb=" N GLU A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 732 " --> pdb=" O ASN A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 752 removed outlier: 3.510A pdb=" N GLU A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 876 Processing helix chain 'A' and resid 880 through 918 removed outlier: 3.906A pdb=" N LEU A 884 " --> pdb=" O ASN A 880 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A 912 " --> pdb=" O ASP A 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.971A pdb=" N PHE D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 135 through 143 Processing helix chain 'D' and resid 145 through 153 Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 257 through 265 removed outlier: 3.668A pdb=" N LYS D 261 " --> pdb=" O ASP D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 281 Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.776A pdb=" N LEU D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 311 removed outlier: 3.638A pdb=" N ASN D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 335 removed outlier: 4.084A pdb=" N TYR D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 329 " --> pdb=" O CYS D 325 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU D 335 " --> pdb=" O GLY D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 347 removed outlier: 3.649A pdb=" N VAL D 342 " --> pdb=" O ASN D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 372 removed outlier: 3.507A pdb=" N LEU D 368 " --> pdb=" O SER D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.604A pdb=" N VAL D 378 " --> pdb=" O VAL D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 393 removed outlier: 4.004A pdb=" N GLN D 386 " --> pdb=" O ASN D 382 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 393 " --> pdb=" O SER D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 416 removed outlier: 3.875A pdb=" N LEU D 408 " --> pdb=" O ALA D 404 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL D 410 " --> pdb=" O LYS D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 427 Processing helix chain 'D' and resid 438 through 460 Processing helix chain 'D' and resid 461 through 465 removed outlier: 3.767A pdb=" N ARG D 464 " --> pdb=" O ALA D 461 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 465 " --> pdb=" O ALA D 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 461 through 465' Processing helix chain 'D' and resid 483 through 488 removed outlier: 4.090A pdb=" N LYS D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR D 488 " --> pdb=" O PHE D 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 483 through 488' Processing helix chain 'D' and resid 492 through 521 removed outlier: 3.767A pdb=" N GLU D 512 " --> pdb=" O ALA D 508 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TRP D 514 " --> pdb=" O CYS D 510 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR D 515 " --> pdb=" O LYS D 511 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Proline residue: D 518 - end of helix removed outlier: 3.506A pdb=" N TYR D 521 " --> pdb=" O GLY D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 558 removed outlier: 3.842A pdb=" N LEU D 529 " --> pdb=" O LEU D 525 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE D 558 " --> pdb=" O ALA D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 606 removed outlier: 3.750A pdb=" N SER D 595 " --> pdb=" O PRO D 591 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 617 removed outlier: 3.675A pdb=" N ILE D 610 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 611 " --> pdb=" O SER D 608 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU D 614 " --> pdb=" O ALA D 611 " (cutoff:3.500A) Proline residue: D 615 - end of helix Processing helix chain 'D' and resid 620 through 631 removed outlier: 3.652A pdb=" N GLN D 624 " --> pdb=" O PHE D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 634 No H-bonds generated for 'chain 'D' and resid 632 through 634' Processing helix chain 'D' and resid 636 through 657 removed outlier: 3.980A pdb=" N ILE D 640 " --> pdb=" O LYS D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 681 removed outlier: 3.924A pdb=" N TRP D 680 " --> pdb=" O LYS D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 692 removed outlier: 3.735A pdb=" N VAL D 691 " --> pdb=" O VAL D 688 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL D 692 " --> pdb=" O LYS D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 732 removed outlier: 3.580A pdb=" N GLU D 701 " --> pdb=" O HIS D 697 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN D 732 " --> pdb=" O ASN D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 752 removed outlier: 3.509A pdb=" N GLU D 741 " --> pdb=" O ASP D 737 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP D 742 " --> pdb=" O ALA D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 876 Processing helix chain 'D' and resid 880 through 918 removed outlier: 3.906A pdb=" N LEU D 884 " --> pdb=" O ASN D 880 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU D 912 " --> pdb=" O ASP D 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.970A pdb=" N PHE B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'B' and resid 160 through 172 Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 257 through 265 removed outlier: 3.667A pdb=" N LYS B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 281 Processing helix chain 'B' and resid 282 through 290 removed outlier: 3.776A pdb=" N LEU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 311 removed outlier: 3.639A pdb=" N ASN B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 335 removed outlier: 4.084A pdb=" N TYR B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 329 " --> pdb=" O CYS B 325 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.649A pdb=" N VAL B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 removed outlier: 3.507A pdb=" N LEU B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.603A pdb=" N VAL B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 393 removed outlier: 4.004A pdb=" N GLN B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 416 removed outlier: 3.876A pdb=" N LEU B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 427 Processing helix chain 'B' and resid 438 through 460 Processing helix chain 'B' and resid 461 through 465 removed outlier: 3.768A pdb=" N ARG B 464 " --> pdb=" O ALA B 461 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 465 " --> pdb=" O ALA B 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 461 through 465' Processing helix chain 'B' and resid 483 through 488 removed outlier: 4.089A pdb=" N LYS B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 488 " --> pdb=" O PHE B 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 483 through 488' Processing helix chain 'B' and resid 492 through 521 removed outlier: 3.767A pdb=" N GLU B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TRP B 514 " --> pdb=" O CYS B 510 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR B 515 " --> pdb=" O LYS B 511 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Proline residue: B 518 - end of helix removed outlier: 3.505A pdb=" N TYR B 521 " --> pdb=" O GLY B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 558 removed outlier: 3.842A pdb=" N LEU B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 606 removed outlier: 3.750A pdb=" N SER B 595 " --> pdb=" O PRO B 591 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE B 601 " --> pdb=" O GLY B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 removed outlier: 3.674A pdb=" N ILE B 610 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 611 " --> pdb=" O SER B 608 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B 614 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Proline residue: B 615 - end of helix Processing helix chain 'B' and resid 620 through 631 removed outlier: 3.652A pdb=" N GLN B 624 " --> pdb=" O PHE B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 636 through 657 removed outlier: 3.980A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 681 removed outlier: 3.924A pdb=" N TRP B 680 " --> pdb=" O LYS B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 removed outlier: 3.735A pdb=" N VAL B 691 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 692 " --> pdb=" O LYS B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 732 removed outlier: 3.580A pdb=" N GLU B 701 " --> pdb=" O HIS B 697 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 732 " --> pdb=" O ASN B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 752 removed outlier: 3.509A pdb=" N GLU B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP B 742 " --> pdb=" O ALA B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 876 Processing helix chain 'B' and resid 880 through 918 removed outlier: 3.905A pdb=" N LEU B 884 " --> pdb=" O ASN B 880 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU B 912 " --> pdb=" O ASP B 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 removed outlier: 3.970A pdb=" N PHE C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 135 through 143 Processing helix chain 'C' and resid 145 through 153 Processing helix chain 'C' and resid 160 through 172 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 221 through 229 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 257 through 265 removed outlier: 3.668A pdb=" N LYS C 261 " --> pdb=" O ASP C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.776A pdb=" N LEU C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 311 removed outlier: 3.639A pdb=" N ASN C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 335 removed outlier: 4.085A pdb=" N TYR C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 320 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 329 " --> pdb=" O CYS C 325 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 335 " --> pdb=" O GLY C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 removed outlier: 3.649A pdb=" N VAL C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 372 removed outlier: 3.508A pdb=" N LEU C 368 " --> pdb=" O SER C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.604A pdb=" N VAL C 378 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 393 removed outlier: 4.004A pdb=" N GLN C 386 " --> pdb=" O ASN C 382 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 393 " --> pdb=" O SER C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 416 removed outlier: 3.876A pdb=" N LEU C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL C 410 " --> pdb=" O LYS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 Processing helix chain 'C' and resid 438 through 460 Processing helix chain 'C' and resid 461 through 465 removed outlier: 3.768A pdb=" N ARG C 464 " --> pdb=" O ALA C 461 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE C 465 " --> pdb=" O ALA C 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 461 through 465' Processing helix chain 'C' and resid 483 through 488 removed outlier: 4.089A pdb=" N LYS C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C 488 " --> pdb=" O PHE C 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 483 through 488' Processing helix chain 'C' and resid 492 through 521 removed outlier: 3.767A pdb=" N GLU C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TRP C 514 " --> pdb=" O CYS C 510 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR C 515 " --> pdb=" O LYS C 511 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 516 " --> pdb=" O GLU C 512 " (cutoff:3.500A) Proline residue: C 518 - end of helix removed outlier: 3.506A pdb=" N TYR C 521 " --> pdb=" O GLY C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 558 removed outlier: 3.843A pdb=" N LEU C 529 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C 558 " --> pdb=" O ALA C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 606 removed outlier: 3.750A pdb=" N SER C 595 " --> pdb=" O PRO C 591 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE C 601 " --> pdb=" O GLY C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 617 removed outlier: 3.676A pdb=" N ILE C 610 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 611 " --> pdb=" O SER C 608 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU C 614 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Proline residue: C 615 - end of helix Processing helix chain 'C' and resid 620 through 631 removed outlier: 3.652A pdb=" N GLN C 624 " --> pdb=" O PHE C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 636 through 657 removed outlier: 3.981A pdb=" N ILE C 640 " --> pdb=" O LYS C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 681 removed outlier: 3.923A pdb=" N TRP C 680 " --> pdb=" O LYS C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 692 removed outlier: 3.736A pdb=" N VAL C 691 " --> pdb=" O VAL C 688 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 692 " --> pdb=" O LYS C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 732 removed outlier: 3.580A pdb=" N GLU C 701 " --> pdb=" O HIS C 697 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C 732 " --> pdb=" O ASN C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 752 removed outlier: 3.510A pdb=" N GLU C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TRP C 742 " --> pdb=" O ALA C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 876 Processing helix chain 'C' and resid 880 through 918 removed outlier: 3.906A pdb=" N LEU C 884 " --> pdb=" O ASN C 880 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU C 912 " --> pdb=" O ASP C 908 " (cutoff:3.500A) 1340 hydrogen bonds defined for protein. 3980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.95 Time building geometry restraints manager: 9.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3652 1.31 - 1.44: 6468 1.44 - 1.56: 13384 1.56 - 1.69: 108 1.69 - 1.82: 248 Bond restraints: 23860 Sorted by residual: bond pdb=" C07 R0D D1003 " pdb=" N06 R0D D1003 " ideal model delta sigma weight residual 1.278 1.468 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C07 R0D B1001 " pdb=" N06 R0D B1001 " ideal model delta sigma weight residual 1.278 1.468 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C07 R0D C1001 " pdb=" N06 R0D C1001 " ideal model delta sigma weight residual 1.278 1.468 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C07 R0D A1003 " pdb=" N06 R0D A1003 " ideal model delta sigma weight residual 1.278 1.468 -0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" O5 SBM C1003 " pdb=" P SBM C1003 " ideal model delta sigma weight residual 1.648 1.777 -0.129 2.00e-02 2.50e+03 4.14e+01 ... (remaining 23855 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.49: 612 106.49 - 113.54: 12860 113.54 - 120.59: 10496 120.59 - 127.64: 8204 127.64 - 134.69: 208 Bond angle restraints: 32380 Sorted by residual: angle pdb=" C ASN D 110 " pdb=" N ILE D 111 " pdb=" CA ILE D 111 " ideal model delta sigma weight residual 120.24 124.25 -4.01 6.30e-01 2.52e+00 4.04e+01 angle pdb=" C ASN A 110 " pdb=" N ILE A 111 " pdb=" CA ILE A 111 " ideal model delta sigma weight residual 120.24 124.25 -4.01 6.30e-01 2.52e+00 4.04e+01 angle pdb=" C ASN C 110 " pdb=" N ILE C 111 " pdb=" CA ILE C 111 " ideal model delta sigma weight residual 120.24 124.24 -4.00 6.30e-01 2.52e+00 4.04e+01 angle pdb=" C ASN B 110 " pdb=" N ILE B 111 " pdb=" CA ILE B 111 " ideal model delta sigma weight residual 120.24 124.24 -4.00 6.30e-01 2.52e+00 4.04e+01 angle pdb=" N ASN C 125 " pdb=" CA ASN C 125 " pdb=" CB ASN C 125 " ideal model delta sigma weight residual 110.37 101.13 9.24 1.65e+00 3.67e-01 3.13e+01 ... (remaining 32375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 14308 35.90 - 71.80: 284 71.80 - 107.71: 20 107.71 - 143.61: 0 143.61 - 179.51: 4 Dihedral angle restraints: 14616 sinusoidal: 5956 harmonic: 8660 Sorted by residual: dihedral pdb=" N ASN C 125 " pdb=" C ASN C 125 " pdb=" CA ASN C 125 " pdb=" CB ASN C 125 " ideal model delta harmonic sigma weight residual 122.80 107.99 14.81 0 2.50e+00 1.60e-01 3.51e+01 dihedral pdb=" N ASN A 125 " pdb=" C ASN A 125 " pdb=" CA ASN A 125 " pdb=" CB ASN A 125 " ideal model delta harmonic sigma weight residual 122.80 108.00 14.80 0 2.50e+00 1.60e-01 3.50e+01 dihedral pdb=" N ASN B 125 " pdb=" C ASN B 125 " pdb=" CA ASN B 125 " pdb=" CB ASN B 125 " ideal model delta harmonic sigma weight residual 122.80 108.00 14.80 0 2.50e+00 1.60e-01 3.50e+01 ... (remaining 14613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3377 0.090 - 0.180: 235 0.180 - 0.270: 36 0.270 - 0.360: 24 0.360 - 0.450: 4 Chirality restraints: 3676 Sorted by residual: chirality pdb=" C2 SBM D1001 " pdb=" C1 SBM D1001 " pdb=" C3 SBM D1001 " pdb=" O2 SBM D1001 " both_signs ideal model delta sigma weight residual False 2.35 2.80 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" C2 SBM B1003 " pdb=" C1 SBM B1003 " pdb=" C3 SBM B1003 " pdb=" O2 SBM B1003 " both_signs ideal model delta sigma weight residual False 2.35 2.80 -0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" C2 SBM A1001 " pdb=" C1 SBM A1001 " pdb=" C3 SBM A1001 " pdb=" O2 SBM A1001 " both_signs ideal model delta sigma weight residual False 2.35 2.80 -0.45 2.00e-01 2.50e+01 5.03e+00 ... (remaining 3673 not shown) Planarity restraints: 3992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 R0D B1001 " 0.005 2.00e-02 2.50e+03 5.08e-01 7.76e+03 pdb=" C03 R0D B1001 " -0.002 2.00e-02 2.50e+03 pdb=" C04 R0D B1001 " -0.007 2.00e-02 2.50e+03 pdb=" C05 R0D B1001 " -0.007 2.00e-02 2.50e+03 pdb=" C07 R0D B1001 " 0.169 2.00e-02 2.50e+03 pdb=" C08 R0D B1001 " -0.006 2.00e-02 2.50e+03 pdb=" C09 R0D B1001 " 1.156 2.00e-02 2.50e+03 pdb=" C25 R0D B1001 " -1.318 2.00e-02 2.50e+03 pdb=" C26 R0D B1001 " 0.002 2.00e-02 2.50e+03 pdb=" C27 R0D B1001 " 0.005 2.00e-02 2.50e+03 pdb=" N06 R0D B1001 " -0.011 2.00e-02 2.50e+03 pdb="CL01 R0D B1001 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 R0D C1001 " -0.005 2.00e-02 2.50e+03 5.08e-01 7.76e+03 pdb=" C03 R0D C1001 " 0.002 2.00e-02 2.50e+03 pdb=" C04 R0D C1001 " 0.007 2.00e-02 2.50e+03 pdb=" C05 R0D C1001 " 0.007 2.00e-02 2.50e+03 pdb=" C07 R0D C1001 " -0.169 2.00e-02 2.50e+03 pdb=" C08 R0D C1001 " 0.006 2.00e-02 2.50e+03 pdb=" C09 R0D C1001 " -1.156 2.00e-02 2.50e+03 pdb=" C25 R0D C1001 " 1.318 2.00e-02 2.50e+03 pdb=" C26 R0D C1001 " -0.002 2.00e-02 2.50e+03 pdb=" C27 R0D C1001 " -0.005 2.00e-02 2.50e+03 pdb=" N06 R0D C1001 " 0.011 2.00e-02 2.50e+03 pdb="CL01 R0D C1001 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 R0D D1003 " -0.005 2.00e-02 2.50e+03 5.08e-01 7.76e+03 pdb=" C03 R0D D1003 " 0.001 2.00e-02 2.50e+03 pdb=" C04 R0D D1003 " 0.007 2.00e-02 2.50e+03 pdb=" C05 R0D D1003 " 0.007 2.00e-02 2.50e+03 pdb=" C07 R0D D1003 " -0.169 2.00e-02 2.50e+03 pdb=" C08 R0D D1003 " 0.006 2.00e-02 2.50e+03 pdb=" C09 R0D D1003 " -1.156 2.00e-02 2.50e+03 pdb=" C25 R0D D1003 " 1.318 2.00e-02 2.50e+03 pdb=" C26 R0D D1003 " -0.002 2.00e-02 2.50e+03 pdb=" C27 R0D D1003 " -0.005 2.00e-02 2.50e+03 pdb=" N06 R0D D1003 " 0.011 2.00e-02 2.50e+03 pdb="CL01 R0D D1003 " -0.013 2.00e-02 2.50e+03 ... (remaining 3989 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6997 2.82 - 3.34: 20229 3.34 - 3.86: 37007 3.86 - 4.38: 44278 4.38 - 4.90: 75585 Nonbonded interactions: 184096 Sorted by model distance: nonbonded pdb=" OD1 ASP D 265 " pdb=" OG1 THR C 339 " model vdw 2.298 2.440 nonbonded pdb=" OG1 THR A 339 " pdb=" OD1 ASP B 265 " model vdw 2.300 2.440 nonbonded pdb=" OG1 THR B 339 " pdb=" OD1 ASP C 265 " model vdw 2.300 2.440 nonbonded pdb=" OD1 ASP A 265 " pdb=" OG1 THR D 339 " model vdw 2.303 2.440 nonbonded pdb=" OH TYR C 656 " pdb=" O VAL C 691 " model vdw 2.320 2.440 ... (remaining 184091 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 85 through 445 or resid 447 through 920 or resid 1002 or r \ esid 1004)) selection = (chain 'B' and (resid 85 through 445 or resid 447 through 920 or resid 1002 or r \ esid 1004)) selection = (chain 'C' and (resid 85 through 445 or resid 447 through 920 or resid 1002 or r \ esid 1004)) selection = (chain 'D' and (resid 85 through 445 or resid 447 through 920 or resid 1002 or r \ esid 1004)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.380 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 73.250 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.190 23860 Z= 0.513 Angle : 1.046 15.437 32380 Z= 0.524 Chirality : 0.059 0.450 3676 Planarity : 0.018 0.508 3992 Dihedral : 14.599 179.509 8988 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.17 % Allowed : 2.62 % Favored : 97.21 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.12), residues: 2908 helix: -2.19 (0.09), residues: 2020 sheet: None (None), residues: 0 loop : -2.64 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 391 HIS 0.003 0.001 HIS A 183 PHE 0.022 0.002 PHE C 537 TYR 0.039 0.003 TYR D 209 ARG 0.008 0.001 ARG D 583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 393 time to evaluate : 2.577 Fit side-chains REVERT: A 131 TYR cc_start: 0.8502 (p90) cc_final: 0.8010 (p90) REVERT: A 393 GLU cc_start: 0.7029 (tt0) cc_final: 0.6724 (tt0) REVERT: A 407 PHE cc_start: 0.7113 (t80) cc_final: 0.6749 (m-80) REVERT: A 441 MET cc_start: 0.8128 (mmm) cc_final: 0.7899 (mmm) REVERT: A 486 MET cc_start: 0.8126 (mmm) cc_final: 0.7895 (mmm) REVERT: A 494 MET cc_start: 0.7500 (mtt) cc_final: 0.7204 (mmm) REVERT: A 524 GLU cc_start: 0.7947 (tt0) cc_final: 0.7674 (tt0) REVERT: A 530 ASP cc_start: 0.7581 (m-30) cc_final: 0.7335 (m-30) REVERT: A 643 MET cc_start: 0.8358 (mtt) cc_final: 0.7904 (mtt) REVERT: A 666 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7538 (mm-30) REVERT: A 878 GLU cc_start: 0.6566 (pt0) cc_final: 0.6263 (pt0) REVERT: D 131 TYR cc_start: 0.8508 (p90) cc_final: 0.8056 (p90) REVERT: D 393 GLU cc_start: 0.7037 (tt0) cc_final: 0.6731 (tt0) REVERT: D 407 PHE cc_start: 0.7124 (t80) cc_final: 0.6749 (m-80) REVERT: D 441 MET cc_start: 0.8128 (mmm) cc_final: 0.7903 (mmm) REVERT: D 486 MET cc_start: 0.8126 (mmm) cc_final: 0.7903 (mmm) REVERT: D 494 MET cc_start: 0.7507 (mtt) cc_final: 0.7205 (mmm) REVERT: D 524 GLU cc_start: 0.7949 (tt0) cc_final: 0.7677 (tt0) REVERT: D 530 ASP cc_start: 0.7578 (m-30) cc_final: 0.7338 (m-30) REVERT: D 643 MET cc_start: 0.8391 (mtt) cc_final: 0.7935 (mtt) REVERT: D 666 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7538 (mm-30) REVERT: D 878 GLU cc_start: 0.6561 (pt0) cc_final: 0.6260 (pt0) REVERT: B 131 TYR cc_start: 0.8508 (p90) cc_final: 0.8004 (p90) REVERT: B 393 GLU cc_start: 0.7032 (tt0) cc_final: 0.6726 (tt0) REVERT: B 407 PHE cc_start: 0.7114 (t80) cc_final: 0.6750 (m-80) REVERT: B 441 MET cc_start: 0.8130 (mmm) cc_final: 0.7902 (mmm) REVERT: B 486 MET cc_start: 0.8126 (mmm) cc_final: 0.7902 (mmm) REVERT: B 494 MET cc_start: 0.7495 (mtt) cc_final: 0.7196 (mmm) REVERT: B 524 GLU cc_start: 0.7948 (tt0) cc_final: 0.7675 (tt0) REVERT: B 530 ASP cc_start: 0.7584 (m-30) cc_final: 0.7336 (m-30) REVERT: B 643 MET cc_start: 0.8358 (mtt) cc_final: 0.7905 (mtt) REVERT: B 666 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7537 (mm-30) REVERT: B 878 GLU cc_start: 0.6570 (pt0) cc_final: 0.6266 (pt0) REVERT: C 131 TYR cc_start: 0.8522 (p90) cc_final: 0.8043 (p90) REVERT: C 393 GLU cc_start: 0.7029 (tt0) cc_final: 0.6719 (tt0) REVERT: C 407 PHE cc_start: 0.7215 (t80) cc_final: 0.6671 (m-80) REVERT: C 441 MET cc_start: 0.8131 (mmm) cc_final: 0.7901 (mmm) REVERT: C 486 MET cc_start: 0.8120 (mmm) cc_final: 0.7889 (mmm) REVERT: C 494 MET cc_start: 0.7501 (mtt) cc_final: 0.7193 (mmm) REVERT: C 524 GLU cc_start: 0.7950 (tt0) cc_final: 0.7676 (tt0) REVERT: C 530 ASP cc_start: 0.7585 (m-30) cc_final: 0.7340 (m-30) REVERT: C 643 MET cc_start: 0.8357 (mtt) cc_final: 0.7903 (mtt) REVERT: C 666 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7534 (mm-30) REVERT: C 878 GLU cc_start: 0.6589 (pt0) cc_final: 0.6296 (pt0) outliers start: 4 outliers final: 8 residues processed: 397 average time/residue: 1.3866 time to fit residues: 626.6314 Evaluate side-chains 306 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 298 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 503 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 88 optimal weight: 0.1980 chunk 139 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 265 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 HIS A 732 GLN D 380 HIS D 732 GLN B 380 HIS B 732 GLN C 260 GLN C 380 HIS C 732 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23860 Z= 0.234 Angle : 1.058 60.649 32380 Z= 0.418 Chirality : 0.039 0.122 3676 Planarity : 0.005 0.057 3992 Dihedral : 11.922 118.718 3960 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.22 % Allowed : 11.17 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 2908 helix: -0.15 (0.11), residues: 2056 sheet: None (None), residues: 0 loop : -2.09 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 391 HIS 0.003 0.001 HIS A 183 PHE 0.015 0.001 PHE C 537 TYR 0.021 0.002 TYR B 705 ARG 0.003 0.000 ARG D 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 302 time to evaluate : 2.462 Fit side-chains REVERT: A 407 PHE cc_start: 0.7247 (t80) cc_final: 0.6638 (m-80) REVERT: A 441 MET cc_start: 0.8349 (mmm) cc_final: 0.7926 (mmm) REVERT: A 524 GLU cc_start: 0.7913 (tt0) cc_final: 0.7663 (tt0) REVERT: A 530 ASP cc_start: 0.7574 (m-30) cc_final: 0.7366 (m-30) REVERT: A 643 MET cc_start: 0.8350 (mtt) cc_final: 0.7921 (mtt) REVERT: A 666 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7504 (mm-30) REVERT: D 407 PHE cc_start: 0.7253 (t80) cc_final: 0.6636 (m-80) REVERT: D 441 MET cc_start: 0.8346 (mmm) cc_final: 0.7925 (mmm) REVERT: D 524 GLU cc_start: 0.7898 (tt0) cc_final: 0.7648 (tt0) REVERT: D 530 ASP cc_start: 0.7581 (m-30) cc_final: 0.7373 (m-30) REVERT: D 643 MET cc_start: 0.8349 (mtt) cc_final: 0.7919 (mtt) REVERT: D 666 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 407 PHE cc_start: 0.7244 (t80) cc_final: 0.6638 (m-80) REVERT: B 441 MET cc_start: 0.8352 (mmm) cc_final: 0.7931 (mmm) REVERT: B 524 GLU cc_start: 0.7906 (tt0) cc_final: 0.7657 (tt0) REVERT: B 530 ASP cc_start: 0.7577 (m-30) cc_final: 0.7368 (m-30) REVERT: B 643 MET cc_start: 0.8349 (mtt) cc_final: 0.7922 (mtt) REVERT: B 666 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7502 (mm-30) REVERT: B 859 MET cc_start: 0.8542 (mmm) cc_final: 0.8276 (mmm) REVERT: C 407 PHE cc_start: 0.7237 (t80) cc_final: 0.6636 (m-80) REVERT: C 524 GLU cc_start: 0.7913 (tt0) cc_final: 0.7665 (tt0) REVERT: C 530 ASP cc_start: 0.7578 (m-30) cc_final: 0.7369 (m-30) REVERT: C 643 MET cc_start: 0.8346 (mtt) cc_final: 0.7917 (mtt) REVERT: C 666 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7501 (mm-30) outliers start: 28 outliers final: 8 residues processed: 318 average time/residue: 1.3963 time to fit residues: 506.0218 Evaluate side-chains 283 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 275 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 220 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 chunk 286 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23860 Z= 0.227 Angle : 1.041 58.494 32380 Z= 0.406 Chirality : 0.040 0.238 3676 Planarity : 0.004 0.051 3992 Dihedral : 11.451 127.541 3948 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.48 % Allowed : 12.61 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 2908 helix: 0.83 (0.11), residues: 2032 sheet: None (None), residues: 0 loop : -1.84 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 391 HIS 0.003 0.001 HIS C 183 PHE 0.017 0.001 PHE C 548 TYR 0.022 0.002 TYR B 209 ARG 0.004 0.000 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 308 time to evaluate : 2.663 Fit side-chains REVERT: A 407 PHE cc_start: 0.7094 (t80) cc_final: 0.6654 (m-80) REVERT: A 441 MET cc_start: 0.8332 (mmm) cc_final: 0.8023 (mmm) REVERT: A 524 GLU cc_start: 0.7852 (tt0) cc_final: 0.7643 (tt0) REVERT: A 530 ASP cc_start: 0.7436 (m-30) cc_final: 0.7205 (m-30) REVERT: A 643 MET cc_start: 0.8333 (mtt) cc_final: 0.7915 (mtt) REVERT: A 666 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7457 (mm-30) REVERT: A 859 MET cc_start: 0.8649 (mmm) cc_final: 0.8301 (mmm) REVERT: D 407 PHE cc_start: 0.7099 (t80) cc_final: 0.6653 (m-80) REVERT: D 441 MET cc_start: 0.8342 (mmm) cc_final: 0.8034 (mmm) REVERT: D 524 GLU cc_start: 0.7846 (tt0) cc_final: 0.7597 (tt0) REVERT: D 530 ASP cc_start: 0.7464 (m-30) cc_final: 0.7222 (m-30) REVERT: D 643 MET cc_start: 0.8331 (mtt) cc_final: 0.7909 (mtt) REVERT: D 666 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7458 (mm-30) REVERT: B 407 PHE cc_start: 0.7092 (t80) cc_final: 0.6653 (m-80) REVERT: B 441 MET cc_start: 0.8333 (mmm) cc_final: 0.8025 (mmm) REVERT: B 524 GLU cc_start: 0.7852 (tt0) cc_final: 0.7640 (tt0) REVERT: B 530 ASP cc_start: 0.7436 (m-30) cc_final: 0.7202 (m-30) REVERT: B 643 MET cc_start: 0.8332 (mtt) cc_final: 0.7914 (mtt) REVERT: B 666 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7454 (mm-30) REVERT: B 859 MET cc_start: 0.8636 (mmm) cc_final: 0.8263 (mmm) REVERT: C 407 PHE cc_start: 0.7085 (t80) cc_final: 0.6652 (m-80) REVERT: C 524 GLU cc_start: 0.7857 (tt0) cc_final: 0.7648 (tt0) REVERT: C 530 ASP cc_start: 0.7440 (m-30) cc_final: 0.7207 (m-30) REVERT: C 643 MET cc_start: 0.8331 (mtt) cc_final: 0.7912 (mtt) REVERT: C 666 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7453 (mm-30) REVERT: C 859 MET cc_start: 0.8647 (mmm) cc_final: 0.8299 (mmm) outliers start: 34 outliers final: 19 residues processed: 320 average time/residue: 1.3265 time to fit residues: 488.2823 Evaluate side-chains 310 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 291 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 874 LYS Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 874 LYS Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 874 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 1.9990 chunk 199 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 266 optimal weight: 9.9990 chunk 282 optimal weight: 0.4980 chunk 139 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23860 Z= 0.199 Angle : 1.025 58.530 32380 Z= 0.396 Chirality : 0.039 0.170 3676 Planarity : 0.004 0.048 3992 Dihedral : 11.041 125.948 3948 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.66 % Allowed : 13.44 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.16), residues: 2908 helix: 1.34 (0.12), residues: 2028 sheet: None (None), residues: 0 loop : -1.58 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 391 HIS 0.003 0.001 HIS C 183 PHE 0.011 0.001 PHE D 537 TYR 0.019 0.001 TYR A 209 ARG 0.005 0.000 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 305 time to evaluate : 2.347 Fit side-chains REVERT: A 407 PHE cc_start: 0.7073 (t80) cc_final: 0.6630 (m-80) REVERT: A 441 MET cc_start: 0.8339 (mmm) cc_final: 0.7970 (mmm) REVERT: A 530 ASP cc_start: 0.7441 (m-30) cc_final: 0.6837 (m-30) REVERT: A 643 MET cc_start: 0.8316 (mtt) cc_final: 0.7894 (mtt) REVERT: A 859 MET cc_start: 0.8654 (mmm) cc_final: 0.8350 (mmm) REVERT: D 407 PHE cc_start: 0.7077 (t80) cc_final: 0.6629 (m-80) REVERT: D 441 MET cc_start: 0.8336 (mmm) cc_final: 0.7961 (mmm) REVERT: D 530 ASP cc_start: 0.7442 (m-30) cc_final: 0.6838 (m-30) REVERT: D 643 MET cc_start: 0.8313 (mtt) cc_final: 0.7891 (mtt) REVERT: D 726 MET cc_start: 0.8097 (mtp) cc_final: 0.7895 (mtm) REVERT: B 407 PHE cc_start: 0.7071 (t80) cc_final: 0.6630 (m-80) REVERT: B 441 MET cc_start: 0.8339 (mmm) cc_final: 0.7960 (mmm) REVERT: B 524 GLU cc_start: 0.7843 (tt0) cc_final: 0.7626 (tt0) REVERT: B 530 ASP cc_start: 0.7441 (m-30) cc_final: 0.6836 (m-30) REVERT: B 643 MET cc_start: 0.8312 (mtt) cc_final: 0.7893 (mtt) REVERT: B 859 MET cc_start: 0.8649 (mmm) cc_final: 0.8296 (mmm) REVERT: C 407 PHE cc_start: 0.7063 (t80) cc_final: 0.6629 (m-80) REVERT: C 524 GLU cc_start: 0.7849 (tt0) cc_final: 0.7632 (tt0) REVERT: C 530 ASP cc_start: 0.7445 (m-30) cc_final: 0.6838 (m-30) REVERT: C 643 MET cc_start: 0.8314 (mtt) cc_final: 0.7892 (mtt) REVERT: C 859 MET cc_start: 0.8661 (mmm) cc_final: 0.8349 (mmm) outliers start: 38 outliers final: 19 residues processed: 322 average time/residue: 1.2949 time to fit residues: 480.3443 Evaluate side-chains 321 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 302 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 593 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 240 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23860 Z= 0.325 Angle : 1.069 58.316 32380 Z= 0.423 Chirality : 0.042 0.266 3676 Planarity : 0.004 0.048 3992 Dihedral : 11.370 126.837 3948 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.14 % Allowed : 13.22 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.16), residues: 2908 helix: 1.24 (0.12), residues: 2028 sheet: None (None), residues: 0 loop : -1.55 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 391 HIS 0.003 0.001 HIS A 183 PHE 0.017 0.002 PHE B 548 TYR 0.026 0.002 TYR D 209 ARG 0.004 0.001 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 299 time to evaluate : 2.619 Fit side-chains REVERT: A 407 PHE cc_start: 0.7018 (t80) cc_final: 0.6533 (m-80) REVERT: A 441 MET cc_start: 0.8366 (mmm) cc_final: 0.8055 (mmm) REVERT: A 530 ASP cc_start: 0.7426 (m-30) cc_final: 0.6862 (m-30) REVERT: A 691 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8788 (m) REVERT: A 874 LYS cc_start: 0.8406 (ttpt) cc_final: 0.7962 (ttmt) REVERT: D 407 PHE cc_start: 0.7021 (t80) cc_final: 0.6533 (m-80) REVERT: D 441 MET cc_start: 0.8364 (mmm) cc_final: 0.8058 (mmm) REVERT: D 530 ASP cc_start: 0.7426 (m-30) cc_final: 0.6849 (m-30) REVERT: D 691 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8786 (m) REVERT: D 874 LYS cc_start: 0.8402 (ttpt) cc_final: 0.7963 (ttmt) REVERT: B 407 PHE cc_start: 0.7017 (t80) cc_final: 0.6533 (m-80) REVERT: B 441 MET cc_start: 0.8367 (mmm) cc_final: 0.8059 (mmm) REVERT: B 530 ASP cc_start: 0.7426 (m-30) cc_final: 0.6846 (m-30) REVERT: B 691 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8789 (m) REVERT: B 859 MET cc_start: 0.8678 (mmm) cc_final: 0.8350 (mmm) REVERT: B 874 LYS cc_start: 0.8376 (ttpt) cc_final: 0.7955 (ttmt) REVERT: C 407 PHE cc_start: 0.7014 (t80) cc_final: 0.6532 (m-80) REVERT: C 530 ASP cc_start: 0.7430 (m-30) cc_final: 0.6865 (m-30) REVERT: C 691 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8786 (m) REVERT: C 874 LYS cc_start: 0.8375 (ttpt) cc_final: 0.7956 (ttmt) outliers start: 49 outliers final: 33 residues processed: 328 average time/residue: 1.3190 time to fit residues: 497.0643 Evaluate side-chains 329 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 292 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 425 TRP Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 425 TRP Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 425 TRP Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 425 TRP Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 691 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 0.8980 chunk 254 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 282 optimal weight: 7.9990 chunk 234 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 148 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23860 Z= 0.150 Angle : 1.011 58.583 32380 Z= 0.385 Chirality : 0.037 0.155 3676 Planarity : 0.004 0.046 3992 Dihedral : 10.342 123.897 3948 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.74 % Allowed : 15.31 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 2908 helix: 1.63 (0.12), residues: 2064 sheet: None (None), residues: 0 loop : -1.35 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 391 HIS 0.002 0.001 HIS A 269 PHE 0.008 0.001 PHE C 764 TYR 0.012 0.001 TYR D 708 ARG 0.006 0.000 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 300 time to evaluate : 2.633 Fit side-chains REVERT: A 259 ASN cc_start: 0.7756 (m-40) cc_final: 0.7196 (p0) REVERT: A 407 PHE cc_start: 0.6997 (t80) cc_final: 0.6624 (m-80) REVERT: A 441 MET cc_start: 0.8318 (mmm) cc_final: 0.8041 (mmm) REVERT: A 874 LYS cc_start: 0.8339 (ttpt) cc_final: 0.7989 (ttmt) REVERT: D 259 ASN cc_start: 0.7755 (m-40) cc_final: 0.7195 (p0) REVERT: D 407 PHE cc_start: 0.6998 (t80) cc_final: 0.6622 (m-80) REVERT: D 441 MET cc_start: 0.8318 (mmm) cc_final: 0.7959 (mmm) REVERT: D 585 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7504 (mmmm) REVERT: D 874 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7986 (ttmt) REVERT: B 259 ASN cc_start: 0.7757 (m-40) cc_final: 0.7197 (p0) REVERT: B 407 PHE cc_start: 0.6995 (t80) cc_final: 0.6624 (m-80) REVERT: B 441 MET cc_start: 0.8319 (mmm) cc_final: 0.7966 (mmm) REVERT: B 726 MET cc_start: 0.8183 (mtp) cc_final: 0.7913 (mtm) REVERT: B 859 MET cc_start: 0.8662 (mmm) cc_final: 0.8363 (mmm) REVERT: B 874 LYS cc_start: 0.8307 (ttpt) cc_final: 0.8001 (ttmt) REVERT: C 259 ASN cc_start: 0.7749 (m-40) cc_final: 0.7196 (p0) REVERT: C 407 PHE cc_start: 0.6990 (t80) cc_final: 0.6623 (m-80) REVERT: C 726 MET cc_start: 0.8175 (mtp) cc_final: 0.7903 (mtm) REVERT: C 874 LYS cc_start: 0.8306 (ttpt) cc_final: 0.8001 (ttmt) outliers start: 17 outliers final: 8 residues processed: 308 average time/residue: 1.2842 time to fit residues: 455.2822 Evaluate side-chains 313 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 305 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 593 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 157 optimal weight: 0.0170 chunk 281 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN D 856 GLN B 856 GLN C 856 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23860 Z= 0.179 Angle : 1.020 58.386 32380 Z= 0.390 Chirality : 0.038 0.161 3676 Planarity : 0.004 0.045 3992 Dihedral : 10.219 124.464 3948 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.83 % Allowed : 15.92 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.16), residues: 2908 helix: 1.79 (0.12), residues: 2052 sheet: None (None), residues: 0 loop : -1.30 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 391 HIS 0.002 0.001 HIS C 183 PHE 0.018 0.001 PHE A 548 TYR 0.015 0.001 TYR B 209 ARG 0.006 0.000 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 304 time to evaluate : 2.815 Fit side-chains REVERT: A 259 ASN cc_start: 0.7751 (m-40) cc_final: 0.7197 (p0) REVERT: A 407 PHE cc_start: 0.6985 (t80) cc_final: 0.6635 (m-80) REVERT: A 441 MET cc_start: 0.8361 (mmm) cc_final: 0.8047 (mmm) REVERT: A 691 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8824 (m) REVERT: A 874 LYS cc_start: 0.8338 (ttpt) cc_final: 0.8009 (ttmt) REVERT: D 259 ASN cc_start: 0.7750 (m-40) cc_final: 0.7196 (p0) REVERT: D 407 PHE cc_start: 0.6987 (t80) cc_final: 0.6634 (m-80) REVERT: D 441 MET cc_start: 0.8298 (mmm) cc_final: 0.8017 (mmm) REVERT: D 691 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8846 (m) REVERT: D 874 LYS cc_start: 0.8317 (ttpt) cc_final: 0.8000 (ttmt) REVERT: B 259 ASN cc_start: 0.7753 (m-40) cc_final: 0.7198 (p0) REVERT: B 407 PHE cc_start: 0.6983 (t80) cc_final: 0.6636 (m-80) REVERT: B 441 MET cc_start: 0.8297 (mmm) cc_final: 0.8017 (mmm) REVERT: B 691 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8815 (m) REVERT: B 874 LYS cc_start: 0.8276 (ttpt) cc_final: 0.7990 (ttmt) REVERT: C 259 ASN cc_start: 0.7701 (m-40) cc_final: 0.7204 (p0) REVERT: C 407 PHE cc_start: 0.6977 (t80) cc_final: 0.6636 (m-80) REVERT: C 691 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8824 (m) REVERT: C 874 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7986 (ttmt) outliers start: 19 outliers final: 12 residues processed: 316 average time/residue: 1.3043 time to fit residues: 474.1285 Evaluate side-chains 313 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 297 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 691 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 221 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN D 856 GLN B 856 GLN C 856 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23860 Z= 0.171 Angle : 1.019 58.425 32380 Z= 0.389 Chirality : 0.038 0.145 3676 Planarity : 0.004 0.045 3992 Dihedral : 10.018 123.843 3948 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.13 % Allowed : 15.84 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.16), residues: 2908 helix: 1.89 (0.12), residues: 2052 sheet: None (None), residues: 0 loop : -1.25 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 391 HIS 0.002 0.001 HIS A 183 PHE 0.010 0.001 PHE B 419 TYR 0.014 0.001 TYR B 209 ARG 0.007 0.000 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 293 time to evaluate : 2.776 Fit side-chains REVERT: A 259 ASN cc_start: 0.7752 (m-40) cc_final: 0.7199 (p0) REVERT: A 407 PHE cc_start: 0.6971 (t80) cc_final: 0.6639 (m-80) REVERT: A 691 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8827 (m) REVERT: A 874 LYS cc_start: 0.8251 (ttpt) cc_final: 0.7988 (ttmt) REVERT: D 259 ASN cc_start: 0.7751 (m-40) cc_final: 0.7198 (p0) REVERT: D 407 PHE cc_start: 0.6971 (t80) cc_final: 0.6638 (m-80) REVERT: D 691 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8828 (m) REVERT: D 874 LYS cc_start: 0.8252 (ttpt) cc_final: 0.7987 (ttmt) REVERT: B 259 ASN cc_start: 0.7754 (m-40) cc_final: 0.7200 (p0) REVERT: B 407 PHE cc_start: 0.6967 (t80) cc_final: 0.6639 (m-80) REVERT: B 441 MET cc_start: 0.8381 (mmm) cc_final: 0.8066 (mmm) REVERT: B 691 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8822 (m) REVERT: B 874 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7985 (ttmt) REVERT: C 259 ASN cc_start: 0.7693 (m-40) cc_final: 0.7183 (p0) REVERT: C 407 PHE cc_start: 0.6960 (t80) cc_final: 0.6639 (m-80) REVERT: C 691 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8830 (m) REVERT: C 874 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7983 (ttmt) outliers start: 26 outliers final: 19 residues processed: 312 average time/residue: 1.2935 time to fit residues: 464.3779 Evaluate side-chains 310 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 287 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 691 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 0.9990 chunk 269 optimal weight: 0.9990 chunk 245 optimal weight: 8.9990 chunk 262 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 248 optimal weight: 0.5980 chunk 261 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23860 Z= 0.221 Angle : 1.037 58.361 32380 Z= 0.400 Chirality : 0.039 0.190 3676 Planarity : 0.004 0.045 3992 Dihedral : 10.103 124.306 3948 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.31 % Allowed : 15.88 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.16), residues: 2908 helix: 1.81 (0.12), residues: 2056 sheet: None (None), residues: 0 loop : -1.30 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 391 HIS 0.003 0.001 HIS D 183 PHE 0.020 0.001 PHE D 548 TYR 0.019 0.002 TYR B 209 ARG 0.008 0.000 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 305 time to evaluate : 2.133 Fit side-chains REVERT: A 259 ASN cc_start: 0.7752 (m-40) cc_final: 0.7197 (p0) REVERT: A 407 PHE cc_start: 0.7006 (t80) cc_final: 0.6636 (m-80) REVERT: A 530 ASP cc_start: 0.7440 (m-30) cc_final: 0.6819 (m-30) REVERT: A 691 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8819 (m) REVERT: A 874 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7982 (ttmt) REVERT: D 259 ASN cc_start: 0.7753 (m-40) cc_final: 0.7199 (p0) REVERT: D 407 PHE cc_start: 0.7005 (t80) cc_final: 0.6635 (m-80) REVERT: D 530 ASP cc_start: 0.7445 (m-30) cc_final: 0.6853 (m-30) REVERT: D 691 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8817 (m) REVERT: D 874 LYS cc_start: 0.8279 (ttpt) cc_final: 0.7984 (ttmt) REVERT: B 259 ASN cc_start: 0.7754 (m-40) cc_final: 0.7198 (p0) REVERT: B 407 PHE cc_start: 0.7001 (t80) cc_final: 0.6636 (m-80) REVERT: B 530 ASP cc_start: 0.7446 (m-30) cc_final: 0.6854 (m-30) REVERT: B 691 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8842 (m) REVERT: B 874 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7962 (ttmt) REVERT: C 259 ASN cc_start: 0.7689 (m-40) cc_final: 0.7183 (p0) REVERT: C 407 PHE cc_start: 0.6991 (t80) cc_final: 0.6635 (m-80) REVERT: C 530 ASP cc_start: 0.7445 (m-30) cc_final: 0.6855 (m-30) REVERT: C 691 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8819 (m) REVERT: C 874 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7961 (ttmt) outliers start: 30 outliers final: 18 residues processed: 330 average time/residue: 1.2611 time to fit residues: 481.0895 Evaluate side-chains 322 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 300 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 878 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN D 856 GLN B 856 GLN C 856 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23860 Z= 0.168 Angle : 1.021 58.445 32380 Z= 0.389 Chirality : 0.038 0.146 3676 Planarity : 0.004 0.064 3992 Dihedral : 9.821 123.008 3948 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.05 % Allowed : 16.23 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.16), residues: 2908 helix: 1.97 (0.12), residues: 2052 sheet: None (None), residues: 0 loop : -1.25 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 391 HIS 0.002 0.001 HIS B 269 PHE 0.011 0.001 PHE D 419 TYR 0.013 0.001 TYR C 209 ARG 0.016 0.000 ARG C 437 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 291 time to evaluate : 2.541 Fit side-chains REVERT: A 259 ASN cc_start: 0.7748 (m-40) cc_final: 0.7202 (p0) REVERT: A 407 PHE cc_start: 0.6950 (t80) cc_final: 0.6626 (m-80) REVERT: A 530 ASP cc_start: 0.7482 (m-30) cc_final: 0.6885 (m-30) REVERT: A 691 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8840 (m) REVERT: A 874 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7991 (ttmt) REVERT: D 259 ASN cc_start: 0.7747 (m-40) cc_final: 0.7202 (p0) REVERT: D 407 PHE cc_start: 0.6950 (t80) cc_final: 0.6625 (m-80) REVERT: D 530 ASP cc_start: 0.7484 (m-30) cc_final: 0.6887 (m-30) REVERT: D 691 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8841 (m) REVERT: D 874 LYS cc_start: 0.8248 (ttpt) cc_final: 0.7993 (ttmt) REVERT: D 916 LEU cc_start: 0.6070 (tt) cc_final: 0.5560 (tp) REVERT: B 259 ASN cc_start: 0.7747 (m-40) cc_final: 0.7201 (p0) REVERT: B 407 PHE cc_start: 0.6946 (t80) cc_final: 0.6627 (m-80) REVERT: B 530 ASP cc_start: 0.7481 (m-30) cc_final: 0.6888 (m-30) REVERT: B 691 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8841 (m) REVERT: B 874 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7970 (ttmt) REVERT: B 916 LEU cc_start: 0.6065 (tt) cc_final: 0.5556 (tp) REVERT: C 259 ASN cc_start: 0.7688 (m-40) cc_final: 0.7186 (p0) REVERT: C 407 PHE cc_start: 0.6939 (t80) cc_final: 0.6627 (m-80) REVERT: C 530 ASP cc_start: 0.7488 (m-30) cc_final: 0.6894 (m-30) REVERT: C 691 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8841 (m) REVERT: C 874 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7971 (ttmt) outliers start: 24 outliers final: 15 residues processed: 311 average time/residue: 1.3339 time to fit residues: 475.5656 Evaluate side-chains 307 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 288 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 691 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 7.9990 chunk 246 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 213 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 232 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 238 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN D 856 GLN B 856 GLN C 856 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.143515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106010 restraints weight = 43399.314| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.43 r_work: 0.2973 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23860 Z= 0.169 Angle : 1.024 58.391 32380 Z= 0.391 Chirality : 0.038 0.145 3676 Planarity : 0.004 0.065 3992 Dihedral : 9.741 122.687 3948 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.22 % Allowed : 16.23 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.16), residues: 2908 helix: 2.02 (0.12), residues: 2052 sheet: None (None), residues: 0 loop : -1.22 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 391 HIS 0.002 0.001 HIS A 183 PHE 0.019 0.001 PHE C 548 TYR 0.014 0.001 TYR B 209 ARG 0.015 0.000 ARG C 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7986.58 seconds wall clock time: 141 minutes 50.09 seconds (8510.09 seconds total)